Department of Biological Science, The University of Tulsa, Tulsa, OK, 74104, USA.
Department of Biological Science, The University of Tulsa, Oliphant Hall, Room N 106, 800 S Tucker Drive, Tulsa, OK, 74104-3189, USA.
Sci Rep. 2021 Sep 22;11(1):18786. doi: 10.1038/s41598-021-98299-9.
Next-generation sequencing is a robust approach to sequence plant virus genomes in a very short amount of time compared to traditional sequencing methods. Maize dwarf mosaic virus (MDMV) is one of the most important plant viruses worldwide and a significant threat to maize production. In this study, we sequenced 19 MDMV isolates (10 from Johnsongrass and 9 from maize) collected in Oklahoma and Missouri during 2017-2019 using Illumina sequencing and determined the genetic diversity. Sequence reads were assembled and 19 nearly complete genome sequences of MDMV isolates were obtained. Phylogenetic analysis based on complete genomes nucleotide and amino acid sequences revealed two main clusters and a close evolutionary relationship among 19 MDMV isolates. Statistical analysis of individual genes for site-specific selection revealed that all genes are under negative selection. The fixation index (FST) analysis of the MDMV isolates revealed no gene flow between the two main phylogenetic clusters, which emphasizes the divergence of MDMV isolates from the USA. Among the USA MDMV isolates, the mean genetic distance (d) and nucleotide diversity ((π) were highest in the P1 gene coding region. This is the first detailed study on the evolutionary relationship of MDMV isolates based on the nearly complete genome analysis from maize and Johnsongrass.
与传统测序方法相比，下一代测序技术是一种在极短时间内对植物病毒基因组进行测序的强大方法。玉米矮花叶病毒（MDMV）是全球最重要的植物病毒之一，也是玉米生产的重大威胁。在这项研究中，我们使用 Illumina 测序对 2017 年至 2019 年期间在俄克拉荷马州和密苏里州收集的 19 个 MDMV 分离株（10 个来自约翰逊草，9 个来自玉米）进行了测序，并确定了遗传多样性。对序列读数进行组装，获得了 19 个 MDMV 分离株的近乎完整的基因组序列。基于完整基因组核苷酸和氨基酸序列的系统发育分析显示，19 个 MDMV 分离株分为两个主要聚类群，并且它们之间存在密切的进化关系。对各基因进行的特定位点选择的统计分析表明，所有基因都受到负选择的影响。MDMV 分离株的固定指数（FST）分析表明，两个主要系统发育聚类群之间没有基因流，这强调了 MDMV 分离株与美国的分化。在来自美国的 MDMV 分离株中，P1 基因编码区的平均遗传距离（d）和核苷酸多样性（π）最高。这是首次基于玉米和约翰逊草的近乎完整基因组分析对 MDMV 分离株的进化关系进行的详细研究。
